Insights into the evolutionary history ofCervus(Cervidae, tribe Cervini) based on Bayesian analysis of mitochondrial marker sequences, with first indications for a new species

Abstract

Molecular phylogeny and evolutionary history of Cervus, the most successful and widespread cervid genus, have been extensively addressed in Europe, fairly in eastern Asia, but scarcely in central Asia, where some populations have never been phylogenetically investigated with DNA-based methods. Here, we applied a coalescent Bayesian approach to most Cervus taxa using complete mitochondrial cytochrome b gene and control region to provide a temporal framework for species differentiation and dispersal, with special emphasis on the central Asian populations from the Tarim Basin (C. elaphus bactrianus, C. elaphus yarkandensis) and Indian Kashmir (C. elaphus hanglu) aiming at assessing their phylogenetic and phylogeographic patterns. Red deer (C. elaphus), wapiti (C. canadensis) and sika deer (C. nippon) are confirmed as highly differentiated taxa, with genetic distances, divergence times and phylogenetic positions compatible with the rank of species. Similarly, the red deer of the Tarim group, hitherto considered as subspecies of C. elaphus, showed a comparable pattern of genetic distinction in the phylogeny and, according to our results, are thus worthy of being raised to the species level. The systematic position of the endangered red deer from Indian Kashmir is assessed here for the first time, and implications for its conservation are also outlined. Based on phylogeny and divergence time estimates, we propose a novel evolutionary pattern for the genus Cervus during the Mio/Pliocene, in the light of palaeo-climatological information.

Phylogeography of the Tyrrhenian red deer (Cervus elaphus corsicanus) resolved using ancient DNA of radiocarbon-dated subfossils

“…e . maral 18 that were also found in the present study. The phylogenetic proximity between Mesola and the C lineage would geographically match the presence of C haplotypes in ancient northern Italian red deer found in the present study, not far away from the site of Mesola (see Fig.…”

Subspecies dynamics in space and time: A study of the red deer complex using ancient and modern DNA and morphology

“…hanglu is 17–18 bp away from bactrianus, whereas one sample of yarkandensis differs by only 2 bp from bactrianus (Figure ). Our data support Lorenzini and Garofalo () in placing the endangered hanglu as part of this group, and not with wallichi and macneilli as suggested by Mattioli (), although it is the most genetically divergent of the three. This group is provisionally treated as a species, C. hanglu (IUCN, ). Chinese subspecies ( C. c. xanthopygus , alashanicus , macneilli, wallichi , kansuensis ) form a well‐supported wapitoid clade (97% and 0.95 bootstrap value and posterior probabilities, respectively).…”

“…The divergence time between wapitoids and elaphoids is also contested. Published molecular estimates range from 7–3 Myr (Lorenzini & Garofalo, ; Ludt et al., ), to c . 0.8–0.2 Myr (Kuwayama & Ozawa, ; Polziehn & Strobeck, ).…”

“…In this study, we examine red deer from across its Holarctic range, incorporating modern and ancient DNA to ask whether the present phylogeography has persisted through climatic perturbations or is it a relatively recent phenomenon. We follow Lorenzini and Garofalo () and the IUCN () in recognizing C. elaphus and C. canadensis , and provisionally C. hanglu , as separate species. All are informally named “red deer,” but we retain the term “elaphoids” for C. elaphus and C. hanglu , and “wapitoids” for C. canadensis .…”

Genomic variation across cervid species in respect to the estimation of red deer diversity

“…The phylogenic relationships and genetic diversity, as well as the level of admixture across native populations of the Cervidae family have been investigated primarily based on mitochondrial DNA [14,15] and microsatellite markers [11][12][13]. Profi ling a large number of single nucleotide polymorphisms (SNPs) was only realistically possible for organisms with well-developmed genomic resources, and the high cost of developing these resources has been a major impediment to studies for non-model organisms, e.g.…”